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Escherichia coli K-12 substr. MG1655 Transporter: xanthosine:H+ symporter XapB



Gene: xapB Accession Numbers: EG13159 (EcoCyc), b2406, ECK2400

Synonyms: XapB xanthosine MFS transporter

Regulation Summary Diagram: ?

Summary:
XapB is a probable xanthosine transporter. The xapB gene is located in a xanthosine-inducible operon with xapA, encoding xanthosine phosphorylase [Seeger95]. Growth on xanthosine is greatly reduced in xapB mutants, and XapB was demonstrated to fractionate with the cell membrane. XapB is a member of the major facilitator superfamily of transporters and shares a high degree of similarity with the nucleoside transporter NupG [Pao98]. XapB therefore is probably a xanthosine/proton symporter. Imported xanthosine is cleaved by XapA to yield xanthine which can be used in nucleotide synthesis or as a nitrogen source, and ribose-1-phosphate which can be used as a carbon source.

Locations: inner membrane

Map Position: [2,520,751 <- 2,522,007] (54.33 centisomes)
Length: 1257 bp / 418 aa

Molecular Weight of Polypeptide: 46.14 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007925 , EchoBASE:EB2951 , EcoGene:EG13159 , EcoliWiki:b2406 , ModBase:P45562 , OU-Microarray:b2406 , PortEco:xapB , PR:PRO_000024229 , Protein Model Portal:P45562 , RefSeq:NP_416901 , RegulonDB:EG13159 , String:511145.b2406 , UniProt:P45562

Relationship Links: InterPro:IN-FAMILY:IPR004740 , InterPro:IN-FAMILY:IPR016196 , InterPro:IN-FAMILY:IPR020846 , Pfam:IN-FAMILY:PF03825 , Prosite:IN-FAMILY:PS50850

Gene-Reaction Schematic: ?

Instance reactions of [a nucleoside[periplasmic space] + H+[periplasmic space] → a nucleoside[cytosol] + H+[cytosol]] (no EC#):
i1: uridine[periplasmic space] + H+[periplasmic space] → uridine[cytosol] + H+[cytosol] (no EC#)

i2: thymidine[periplasmic space] + H+[periplasmic space] → thymidine[cytosol] + H+[cytosol] (no EC#)

i3: inosine[periplasmic space] + H+[periplasmic space] → inosine[cytosol] + H+[cytosol] (no EC#)

i4: 2'-deoxyuridine[periplasmic space] + H+[periplasmic space] → 2'-deoxyuridine[cytosol] + H+[cytosol] (no EC#)

i5: 2'-deoxyinosine[periplasmic space] + H+[periplasmic space] → 2'-deoxyinosine[cytosol] + H+[cytosol] (no EC#)

i6: 2'-deoxycytidine[periplasmic space] + H+[periplasmic space] → 2'-deoxycytidine[cytosol] + H+[cytosol] (no EC#)

i7: 2'-deoxyadenosine[periplasmic space] + H+[periplasmic space] → 2'-deoxyadenosine[cytosol] + H+[cytosol] (no EC#)

i8: cytidine[periplasmic space] + H+[periplasmic space] → cytidine[cytosol] + H+[cytosol] (no EC#)

i9: adenosine[periplasmic space] + H+[periplasmic space] → adenosine[cytosol] + H+[cytosol] (no EC#)

i10: xanthosine[periplasmic space] + H+[periplasmic space] → xanthosine[cytosol] + H+[cytosol] (no EC#)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0055086 - nucleobase-containing small molecule metabolic process Inferred from experiment [Seeger95]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, Seeger95]
GO:0015858 - nucleoside transport Inferred by computational analysis [Seeger95]
GO:0015863 - xanthosine transport Inferred by computational analysis [Seeger95]
GO:1901642 - nucleoside transmembrane transport Inferred by computational analysis [Seeger95, GOA01]
Molecular Function: GO:0005337 - nucleoside transmembrane transporter activity Inferred by computational analysis [GOA01, Seeger95]
GO:0015553 - xanthosine transmembrane transporter activity Inferred by computational analysis [Seeger95]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Seeger95]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01, Seeger95]

MultiFun Terms: cell structure membrane
metabolism carbon utilization carbon compounds
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for xapB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Enzymatic reaction of: xanthosine:H+ symporter XapB

Synonyms: transport of xanthosine


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 10 -> 30
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 42 -> 62
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 63 -> 80
[Seeger95, UniProt10a]
Alternate sequence: DKWLRAERAYMLCHLVCA → VQMRARRTCIHAVSPGVC; UniProt: (in Ref. 1; CAA52048);
Transmembrane-Region 71 -> 91
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 92 -> 112
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 137 -> 157
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 160 -> 180
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 210 -> 230
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 255 -> 275
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 278 -> 298
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 293 -> 299
[Seeger95, UniProt10a]
Alternate sequence: LRFGFFA → CALASSP; UniProt: (in Ref. 1; CAA52048);
Transmembrane-Region 307 -> 327
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 310 -> 313
[UniProt09]
UniProt: Poly-Leu; Sequence Annotation Type: compositionally biased region;
Transmembrane-Region 349 -> 369
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 382 -> 402
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2406 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG13159; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Pao98: Pao SS, Paulsen IT, Saier MH (1998). "Major facilitator superfamily." Microbiol Mol Biol Rev 1998;62(1);1-34. PMID: 9529885

Seeger95: Seeger C, Poulsen C, Dandanell G (1995). "Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli." J Bacteriol 177(19);5506-16. PMID: 7559336

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Jorgensen99: Jorgensen C, Dandanell G (1999). "Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR." J Bacteriol 1999;181(14);4397-403. PMID: 10400599


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc13.